Expanding Spatial Genomics to Resolve the Epigenome

Abstract

The genome is not only encoded in linear sequence but also organized into complex 3D structures that regulate cellular identity, genome stability, and disease. While many tools exist to profile either chromatin states or nuclear architecture, current methods struggle to jointly measure genome sequence and spatial organization at high resolution. In this thesis, I present methodological advances that bridge this gap by extending spatial genomics technologies to connect DNA sequence, epigenetic state, and nuclear organization. First, we improve upon in situ genome sequencing by incorporating expansion microscopy, creating Expansion in situ Genome Sequencing (ExIGS), which enables nanoscale imaging of nuclear proteins and sequencing of chromatin fragments within expanded nuclei. We validate this approach in fibroblasts and then apply it to Hutchinson-Gilford progeria syndrome (HGPS) cells, revealing how lamin abnormalities in HGPS generate local hotspots of disrupted euchromatin organization and transcriptional repression. Second, I describe advances to ExIGS as well as other complementary methods that I contributed to during my PhD. Together, these tools expand the resolution and functional contexts in which genome structure can be interrogated. Beyond their technical contributions, these methods reveal how nuclear abnormalities and epigenetic mechanisms reshape genome organization across development, aging, and disease. Collectively, this work establishes new experimental frameworks for connecting sequence and structure, advancing our ability to study the genome in its full spatial context.